JAL-2629 update spikes/mungo to latest

[jalview.git] / src / jalview / datamodel / SequenceGroup.java

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index aebcbb3..b558f40 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -88,11 +88,6 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   private SequenceI seqrep;
 
-  /*
-   * HMM consensus sequence for group (if any)
-   */
-  private SequenceI hmmConsensus;
-
   private int width = -1;
 
   /*
@@ -283,7 +278,6 @@ public class SequenceGroup implements AnnotatedCollectionI
         seqs[ipos].setDescription(seq.getDescription());
         seqs[ipos].setDBRefs(seq.getDBRefs());
         seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
-        seqs[ipos].setIsHMMConsensusSequence(seq.isHMMConsensusSequence());
         if (seq.getDatasetSequence() != null)
         {
           seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
@@ -1600,18 +1594,6 @@ public class SequenceGroup implements AnnotatedCollectionI
     hmmNormaliseSequenceLogo = state;
   }
 
-  @Override
-  public SequenceI getHmmConsensus()
-  {
-    return hmmConsensus;
-  }
-
-  @Override
-  public void setHmmConsensus(SequenceI hmmSeq)
-  {
-    this.hmmConsensus = hmmSeq;
-  }
-
   public ProfilesI getConsensusData()
   {
     return consensusProfiles;
@@ -1627,4 +1609,19 @@ public class SequenceGroup implements AnnotatedCollectionI
     this.hmmProfiles = hmmProfiles;
   }
 
+  @Override
+  public List<SequenceI> getHmmSequences()
+  {
+    List<SequenceI> result = new ArrayList<>();
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      SequenceI seq = sequences.get(i);
+      if (seq.hasHMMProfile())
+      {
+        result.add(seq);
+      }
+    }
+    return result;
+  }
+
 }